Installation
Last Updated: December 2024
Release Date: July 2024
Document Version: 3
The Illumina NextSeq 500/550 Integration v2.4.0 supports the integration between Clarity LIMS and the NextSeq 500/550 instrument. This document provides instructions for installing NextSeq 500/550 Integration v2.4.0. It also describes the components that are installed in the default configuration.
Compatibility
Refer to Compatibility under Instruments & Integrations.
This integration is not fully compatible with NextSeq 500/550 Integration v1.
Supporting Documentation
For details on installed protocols and steps, automations, generated and captured files, and rules and constraints, refer to NextSeq 500/550 v2.4.0 Configuration.
For information on user interaction for each step, validating and troubleshooting the integration, refer to NextSeq 500/550 Integration v2.4.0 User Interaction, Validation and Troubleshooting.
Prerequisites
NextSeq 500/550 Integration v2.4.0 has the following prerequisites:
Mount run data network-attached storage (NAS) share
Secret Util is installed
IPP is installed
Installation
NextSeq 500/550 Integration v2.4.0 is distributed as the ClarityLIMS-Illumina-NextSeq-Package-v2 RPM package that must be installed on the Clarity LIMS server. This package installs the following items:
Bash scripts used to run the service
The nextseq-sequencing.jar file
The configure_extensions_nextseq_sequencingservice.sh script
Smoke test directories
When upgrading from an existing NextSeq 500/550 workflow, the following warning messages can display when the illumina-preset-protocls-installer.sh script is running:
WARN Installer - Conflicting content:
WARN Installer - Analyte UDFs: % Aligned R1
WARN Installer - Analyte UDFs: % Aligned R2
WARN Installer - Analyte UDFs: % Bases >=Q30 R1
WARN Installer - Analyte UDFs: % Bases >=Q30 R2
WARN Installer - Analyte UDFs: Cluster Density (K/mm^2) R1
WARN Installer - Analyte UDFs: Cluster Density (K/mm^2) R2
WARN Installer - Analyte UDFs: Clusters PF R1
WARN Installer - Analyte UDFs: Clusters PF R2
WARN Installer - Analyte UDFs: Clusters Raw R1
WARN Installer - Analyte UDFs: Clusters Raw R2
WARN Installer - Analyte UDFs: Intensity Cycle 1 R1
WARN Installer - Analyte UDFs: Intensity Cycle 1 R2
These messages are due to configuration changes that have increased the precision of the listed fields from 1 to 2 so that they show more decimal places. It is safe to override these warnings.
The following installation steps are required for the installation of NextSeq 500/550 Integration v2.4.0.
Install the RPM
On the Clarity LIMS server, log in as the root user.
Run the following yum command to install the RPM:
ℹ You must use the --enablerepo command line argument to enable the repo. For the repo file and the correct name to use, contact Illumina Support.
yum install ClarityLIMS-Illumina-NextSeq-Package-v2 --enablerepo=< repo name info from support >
Enter y to confirm that you want to proceed with the RPM installation. After confirmation, you are prompted to install the NextSeq 500/550 workflow from the IPP RPM.
ℹ If you have not installed the SecretUtil RPM before, this RPM installation also installs it.
For hosted installations, the Secret Util installation and configuration is handled by tooling.
For on-premise installations, if the Secret Util package is not already installed or configured, you must configure the Secret Util first. For more information, refer to Prerequisite 2: Secret Util Installation in Prerequisites.
Install the NextSeq 500/550 workflow as follows.
As the glsjboss user, run the following command to view the complete list of IPP workflows:
/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o list
Run the following command to install the NextSeq 500/550 Sequencing v1.2 workflow:
/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install Illumina_Instruments.nextseq550-v1.2
[Optional] Run the following command to install the Library Prep Validation v2.3.4 workflow that is used to validate the NextSeq 500/550 Sequencing v1.2 workflow:
/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install Illumina_Instruments.Library-Prep-Validation-v2.3
Run the following script to configure the service properties:
/opt/gls/clarity/config/configure_extensions_nextseq_sequencingservice-v2.sh
Configure the Integration Properties
The integration properties can be configured to enable capture and generation of files associated with the sequencing run. Refer to Integration Properties Details for details.
The property configuration for NextSeq 500/550 v2 has the suffix .v2 and is different from the setting for v1.
Start the Sequencing Service
Run the following command to start the sequencing service:
systemctl start nextseq_seqservice-v2
NextSeq Control Software v4.0 Configuration
In NextSeq Control Software (NCS) v4.0 the location of NextSeq.Configuration.xml RTA configuration file is changed. The new location is
C:\Program Files\Illumina\RTA\2.11.3\Configs
A new gls_events_ncs_rta.bat batch file is required to generate a valid EndRun event file. This file is available in the NextSeq 500/550 RPM at
/opt/gls/clarity/extensions/Illumina_NextSeq/v2/InstrumentIntegrations
Configuration
Download the latest batch file from the NextSeq 500/550 RPM and place it in a folder (e.g., C:\Illumina\gls). If necessary, remove the old batch file.
Edit the NextSeq.Configuration.xml configuration file at
C:\Program Files\Illumina\RTA\2.11.3\Configs
If you cannot modify the file, then open it as an administrator. Insert the following text inside the <Processing> tag. If the batch file is not at C:\Illumina\gls, then change that text to the applicable path.
<PostProcessEventFile>C:\Illumina\gls\gls_event_ncs_rta.bat</PostProcessEventFile>
Save the configuration file.
Validate the file by running RTA manually. In the command prompt, run the following command:
"C:\Program Files\Illumina\RTA\2.11.3\RTA.exe" "." configFile="C:\Program Files\Illumina\RTA\2.11.3\Configs\NextSeq.Configuration.xml" Processing.WorkProviderTypes="OfflineBased" processedfolder="."
The following error message displays:
Error: No run info file found in input directory .\RunInfo.xml
Validate the batch file by executing it manually as follows.
Using a text editor, edit the gls_events_ncs_rta.bat file.
In the "set DESTINATION_PATH=C:\Illumina\gls\Events" code line, change C:\Illumina\gls\Events\ to the network path of the event files directory. Make sure to include the backslash at the end of the file path.
After manually executing the batch file, a dummy EndRun event file is created in the event files directory.

Workflows, Protocols, and Steps Installed
NextSeq 500/550 Integration v2.4.0 works with the NextSeq 500/550 Sequencing v1.2 workflow, which contains a single protocol with the same name. This protocol includes the following steps:
Library Pooling (NextSeq 500/550 v1.2)
Denature & Dilute (NextSeq 500/550 v1.2)
NextSeq 500/550 Run (NextSeq 500/550 v1.2)
For descriptions of the protocol and the steps, refer to NextSeq 500/550 v2.4.0 Configuration. For instructions on using the Library Prep Validation v2.3.4 workflow to validate the automated sample sheet generation, refer to NextSeq 500/550 Integration v2.4.0 User Interaction, Validation and Troubleshooting.
Instrument Software
The NextSeq Control Software (NCS) is divided into the following modules:
NCS — Controls the instrument operation, including various configuration settings. This software is installed and runs on the instrument.
Real-Time Analysis 2 (RTA2) — Performs image processing and base calling (primary analysis). The software makes sure that data files are created and copied to the final destination folder and is installed and runs on the instrument.
For more information on NCS, refer to the NextSeq 500/550 documentation at support.illumina.com.
Instrument Integration
The instrument integration must be performed and maintained by Illumina Support. Illumina Support requires remote access to the instrument while it is idle.
Illumina Support has created batch files that use custom scripts during the key events of a sequencing run. When these batch files are used, they read the event information and write it in a TXT event file at the same network share location that the instrument uses to write the run data. Another process running on the Clarity LIMS server receives the event files and takes the appropriate actions.
The sequencing service monitors the end of the run event. This event is used to capture key step data and files and parse run statistics for output custom fields.
For NextSeq Control Software (NCS) v4.0 and later, refer to the configuration steps in NextSeq Control Software v4.0 Configuration. For NCS versions before v4.0, perform the following steps.
Validation
Revision History
Version
Changes
3
Updated
Compatibility
Prerequisite 3
2
Corrected typo in Prerequisite 3 of Prerequisites section.
1
Initial release.
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